With the emergence of synthetic biology and nanotechnology, systematic alteration of existing cells to produce modified cells is becoming a frequent research goal. However, designing these modified cells may be very challenging in vitro because it often requires expensive and laborious cellular assays. These modified cells are also dangerous; they could have an unpredictable and potentially devastating impact on any ecosystem they might enter. Thus, given the cost and potential danger of designing synthetic cells, a method and system of modeling both natural and synthetically modified cells in silico is desired.
Moreover, there is a need for in silico methods of modeling the effects of chemical compounds and biologic compounds on a natural or synthetically modified cell. Testing of chemical compounds on cells in vitro involves the expense of cellular media and proliferation assays, the constant labor of maintaining cell cultures, and repeating each assay with a different chemical compound to generate data. These procedures are costly and time consuming. Thus, there is a need for a method of modeling cells or a portion of a cell under different conditions in silico rather than in vitro.
Traditional in silico models are based on computer programs capable of modeling a single portion of a cell or a single cell, for example, those programs using the single hierarchical pathway systems of Biopax or SBML. These models may be constraining because a user has to generate a new model for each type of cell or portion of a cell to run a simulation. Further, if a user is interested in altering a portion of a cell to run new simulations, the user may have to deconstruct the model to do so.